Schema for Geneid Genes (BUSCO) - Geneid Gene Predictions with CEGMA Training Set

Database: DpseGB3 Primary Table: geneidCEGMA Row Count: 17,527 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid_cegma-CH379058_1	`varchar(255)`	values
`chrom`	CH379058	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	295	`int(10) unsigned`	range
`txEnd`	557	`int(10) unsigned`	range
`cdsStart`	295	`int(10) unsigned`	range
`cdsEnd`	557	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	295,541,	`longblob`
`exonEnds`	477,557,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-CH379058_1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	1,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	mRNA_geneid_cegma-CH379058_1	CH379058	-	295	557	295	557	2	295,541,	477,557,	geneid_cegma-CH379058_1	unk	unk	1,0,
585	mRNA_geneid_cegma-CH379058_2	CH379058	+	2856	14405	2856	14405	2	2856,14351,	3006,14405,	geneid_cegma-CH379058_2	unk	unk	0,0,
585	mRNA_geneid_cegma-CH379058_3	CH379058	-	17120	22628	17120	22628	1	17120,	22628,	geneid_cegma-CH379058_3	unk	unk	0,
585	mRNA_geneid_cegma-CH379058_4	CH379058	-	26783	42583	26783	42583	3	26783,35723,42476,	26939,35805,42583,	geneid_cegma-CH379058_4	unk	unk	0,2,0,
585	mRNA_geneid_cegma-CH379058_5	CH379058	-	43860	43998	43860	43998	1	43860,	43998,	geneid_cegma-CH379058_5	unk	unk	0,
585	mRNA_geneid_cegma-CH379058_6	CH379058	-	44924	45014	44924	45014	1	44924,	45014,	geneid_cegma-CH379058_6	unk	unk	0,
585	mRNA_geneid_cegma-CH379058_7	CH379058	+	45684	45945	45684	45945	2	45684,45839,	45770,45945,	geneid_cegma-CH379058_7	unk	unk	0,2,
585	mRNA_geneid_cegma-CH379058_8	CH379058	+	47935	48549	47935	48549	2	47935,48541,	48032,48549,	geneid_cegma-CH379058_8	unk	unk	0,1,
585	mRNA_geneid_cegma-CH379058_9	CH379058	+	49114	49327	49114	49327	1	49114,	49327,	geneid_cegma-CH379058_9	unk	unk	0,
585	mRNA_geneid_cegma-CH379058_10	CH379058	+	52434	60888	52434	60888	8	52434,56117,57379,57841,58214,58972,59607,60849,	52481,56215,57776,58152,58256,59324,60676,60888,	geneid_cegma-CH379058_10	unk	unk	0,2,1,2,1,1,2,0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Geneid Genes (BUSCO) (geneidCEGMA) Track Description


	Description This track shows the gene predictions produced by geneid using species-specific parameters. Methods The species-specific geneid parameters were produced by CEGMA. References Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007 May 1;23(9):1061-7. Parra G, Blanco E, Guigó R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5.

Description